Linking from NCBI (Entrez) Gene, UniProt to PC

[GoogleCodeExporter]

We need to link Entrez Gene to pathwaycommons.org

This requires building XML files to submit to Entrez Gene.

We probably want to automatically generate these files with every PC build (and 
include the feature with cpath2 as well, so code should be reuable between 
cpath1 and 2)

Original issue reported on code.google.com by [email protected] on 18 Nov 2010 at 3:16

[GoogleCodeExporter]

To have linkout from the NCBI website to PathwayCommons, NCBI require 2 XML 
files: an identity file and a resource file.

The resource file contains the URL base that is used to make the link and the 
identifiers in pathwaycommons for the each resource in NCBI that we want to  
link to.

The mysql instance on toro contains a development version of the pc database. 
The database has the table external_link.

The resources were extracted from cpath using the following SQL:
select  cpath_id, linked_to_id from external_link where external_db_id =1 into 
outfile 'NCBI_lnfile' and converted from the txt download into the XML using 
XSLT.

The file was validated using the NCBI linkout validator.

2 test files were sent.


Feedback received:
Hi Nadia,

I created an account for your resource. Please use the below information in
your files:

Name: Pathway Commons
Provider Id: 7665
NameAbbr: pathcom

The files need a few edits:

Providerinfo.xml:

1)      Remove:
<SubjectType> metabolic pathways/protein interaction networks/signal
transduction pathways/gene regulatory networks </SubjectType>

Select one subject type for the list provided here:

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helplinkout
<http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helplinkout&part=files#f
iles.Special_Elements_SubjectType>
&part=files#files.Special_Elements_SubjectType

Resources file:

1)      Remove the below from all links:
<UrlName>Pathwy Commons</UrlName>

2)      Use a field qualifier with your queries. Instead of:

<Query>Q9XVB1</Query>

Use:
<Query>Q9XVB1[acc]</Query>

I'll create an FTP account for you and will send details in a separate
email.

Best,

Lidia Hutcherson

Original comment by [email protected] on 18 Nov 2010 at 3:33

[GoogleCodeExporter]

Original comment by [email protected] on 4 Jan 2013 at 4:28

• Added labels: Product-cPath, Product-cPath2, Type-Task
• Removed labels: Project-cPath

[GoogleCodeExporter]

Can add Linking from UniProt to PC2 to this task too...

Original comment by [email protected] on 14 Feb 2013 at 5:22

• Added labels: Milestone-M4

[GoogleCodeExporter]

Original comment by [email protected] on 27 Jun 2014 at 9:53

• Added labels: Product-Collaboration
• Removed labels: Product-cPath, Milestone-M4

[IgorRodchenkov]

And - linking from UniProt to PathwayCommons (e.g., link by primary UniProt accession to the PCViz view for that protein's neighborhood)

[IgorRodchenkov]

@gbader @jvwong @cannin
We can now link a gene ID/symbol to the Pathways search app.

[IgorRodchenkov]

A new issue #294 continues this older one; so closing...